You could each use your entire armies as a maximum pool of available units to draw from in a campaign with set CP points, you'd have to agree to the CP costs for all units in both armies beforehand. Each battles outcome effects the next battle, and the units that survive get added to the next armies total. I'd also use objectives and award one off bonuses for achieving them throughout the campaign.

Yea, I've played a few "Draft Pick" games with some friends, they always turn out fun. We take about 10 min to pick out the teams, you can pick single figures, a squad, or a vehicle, and then you both take about 30 min to set up the battlefield with random ruins. Very Brikwarsy.

I find that with the larger games it helps to split up teams- IE: the " " Air force and the " " Army, or by other lines (give the droids to one guy, the wookies to another, etc) and just have them allied and stuff.